{"id":"W2064604026","doi":"10.1093/nar/gkt1087","title":"TFBSshape: a motif database for DNA shape features of transcription factor binding sites","year":2013,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":128,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"National Institute of General Medical Sciences; National Human Genome Research Institute","keywords":"Biology; Motif (music); Transcription factor; Genetics; DNA binding site; DNA; Computational biology; Sequence motif; Transcription (linguistics); DNA-binding protein; Database; Promoter; Gene; Gene expression; Computer science","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003229255,0.0001314512,0.0001500365,0.0001160403,0.0001458735,0.00006560636,0.0003667728,0.0001709964,0.0002787983],"category_scores_gemma":[0.0001712642,0.0001208849,0.0001071794,0.0001357706,0.0001317315,0.00001143151,0.0001387567,0.0001630618,0.00003129043],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002554914,"about_ca_system_score_gemma":0.0000672177,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003756814,"about_ca_topic_score_gemma":0.00002710718,"domain_scores_codex":[0.998706,0.00006511157,0.0002089616,0.000342663,0.0002701041,0.000407157],"domain_scores_gemma":[0.9990951,0.00004171769,0.00005183992,0.0003890383,0.0003151997,0.0001071259],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0000456728,0.00006592842,0.0009536581,0.00012347,0.00003690955,4.044555e-7,0.0001117438,0.000003491362,0.9886912,0.0001533754,0.003914751,0.005899441],"study_design_scores_gemma":[0.001368679,0.0009908844,0.0292724,0.0000600909,0.00001856969,0.00001024273,0.0008036922,0.009024261,0.9491376,0.000496262,0.008434566,0.0003827812],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9976545,0.0002766115,0.0004232826,0.0001874939,0.00005390331,0.0005827721,0.0003756497,0.000009450478,0.0004363313],"genre_scores_gemma":[0.9947863,0.0001762302,0.003198241,0.00003083568,0.0001310899,0.00007972165,0.0006143564,0.00003779801,0.0009454694],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03955359,"threshold_uncertainty_score":0.4929545,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04148482227225522,"score_gpt":0.3180629021143506,"score_spread":0.2765780798420954,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}